The final solution to BP's oil well spill could be in place by Sunday, five months after the deadly explosion spewed 5m barrels of crude into the Gulf of Mexico, the Obama administration said today.

But officials conceded the effects of the spill, which turned the Gulf of Mexico into an environmental and economic disaster zone and brought one of the world's biggest oil companies to the brink of ruin, would be felt for months, if not years.

Barack Obama's point man on the oil spill, coastguard commander Thad Allen, told reporters in a conference call today that drill crews were hours away from intercepting the Macondo well and installing a permanent plug.

"We started this morning the final drilling process to close in on the bottom of the Macondo well," he said. "Four days from now it could all be done. This is the window we are looking at right now."

Allen said the administration had already begun to move out equipment from the well site, in anticipation of the placement of a permanent mud and cement seal.

He said the central pipe of the well is already under a cement seal, after oil was injected into the top of the well in July. But he said it is unclear whether oil is still flowing in the area between that pipe and the rock formation. But even with the end only hours away, Jane Lubchenco, who heads the National Oceanic and Atmospheric (NOAA) adminstration, said there was still significant oil in the Gulf, especially at depths.

The admission marks a reversal for the rosy assertions by the administration last month that nearly 75% of the oil had been broken down or cleaned up.

"There continues to be some oil in the subsurface especially in this layer between 3,000 to 4,300ft," she said. "There is oil being observed in the sediment on the sea floor surface." Much of that oil is in tiny droplets – the width of a human hair but Lubchenco said that did not diminish its potential impacts.

Scientists on a University of Georgia research voyage reported this week that they had found a two-inch-thick layer of oil on the ocean floor, challenging the NOAA's earlier assertions that the oil was rapidly being broken down.

Lubchenco promised the administration would continue to track the oil over the long term to ensure the health of the marine environment and protect the seafood industry in the Gulf.

Parish officials in Louisiana have reported a number of fish kills in areas affected by the spill and Plaquemines parish reported this week that large numbers of fish had died around Bayou Chaland on the west side of the Mississippi river. The officials said it was unclear whether the fish were killed by contact with oil or because of a drop in oxygen levels caused by high activity among microbes eating up the oil.